Quantitative data analysis methods for bead-based DNA hybridization assays using generic flow cytometry platforms.

Bead-based assays are in demand for rapid genomic and proteomic assays for both research and clinical purposes. Standard quantitative procedures addressing raw data quality and analysis are required to ensure the data are consistent and reproducible across laboratories independent of flow platform. Quantitative procedures have been introduced spanning raw histogram analysis through to absolute target quantitation. These included models developed to estimate the absolute number of sample molecules bound per bead (Langmuir isotherm), relative quantitative comparisons (two-sided t-tests), and statistical analyses investigating the quality of raw fluorescence data. The absolute target quantitation method revealed a concentration range (below probe saturation) of Cy5-labeled synthetic cytokeratin 19 (K19) RNA of c.a. 1 x 10(4) to 500 x 10(4) molecules/bead, with a binding constant of c.a. 1.6 nM. Raw hybridization frequency histograms were observed to be highly reproducible across 10 triplex assay replicates and only three assay replicates were required to distinguish overlapping peaks representing small sequence mismatches. This study provides a quantitative scheme for determining the absolute target concentration in nucleic acid hybridization reactions and the equilibrium binding constants for individual probe/target pairs. It is envisaged that such studies will form the basis of standard analytical procedures for bead-based cytometry assays to ensure reproducibility in inter- and intra-platform comparisons of data between laboratories.

An evaluation of the cell-dyn 3200 for counting cells in cerebrospinal and other body fluids.

This study compared the white blood cell (WBC) and red blood cell (RBC) counts obtained with the Cell-Dyn 3200 (CD 3200) with results obtained by hemocytometer, the reference method for counting cerebrospinal fluid (CSF) and other body fluid specimens. Ninety-six CSF and 65 body fluid specimens were evaluated. Background counts were maintained on the CD 3200 at 0.001 x 10(9)/L and 0.00 x 10(12)/L for WBC and RBC counts, respectively. Linearity and precision were acceptable for both the total nucleated cell (TNC) count and the RBC count. The CD 3200 WBC optical count was correlated with the TNC count obtained by the manual reference method for CSF specimens across the range of 0 x 10(9 )/L to 7.863 x 10(9)/L (r2 = 0.9867) and for body fluid specimens across the range of 0 x 10(9)/L to 14.0 x 10(9)/L (r2 = 0.9955). An r2 value of 0.9016 was obtained for the 82 CSF specimens with manual TNC counts of <0.200 x 10(9)/L. Analysis of the CSF and body fluid specimens indicated that automated RBC counts could be reported at > or = 0.003 x 10(12)/L. In this study, 7 CSF and 30 body fluid specimens had RBC counts of >0.003 x 10(12)/L, and there was good agreement with manual RBC counts, with r2 values of 0.9893 and 0.9960 obtained for CSF and other body fluids, respectively. The CD 3200 in our experience has a lower reportable range than the ranges of most automated cell counters reported in the literature. In contrast to the only other instrument with comparable reportable ranges, the CD 3200 requires a smaller sample volume without any special sample preparation, reagents, or software. By using the CD 3200 with our laboratory-specific rules for agreement between duplicate counts, we would be able to reduce our manual CSF specimen counts from 192 TNC and 192 RBC counts to 2 TNC and 178 RBC counts. For body fluid specimens, our manual counts would be reduced from 130 TNC and 130 RBC counts to 10 TNC and 4 RBC counts.

Identification of genes whose expression patterns differ in benign lymphoid tissue and follicular, mantle cell, and small lymphocytic lymphoma.

Improved methods for diagnosing small B-cell lymphomas (SBCLs) and predicting patient response to therapy are likely to result from the ongoing discovery of molecular markers that better define these malignancies. In this report, we identify 120 genes whose expression patterns differed between reactive lymph node tissue and three types of SBCL: follicular lymphoma, mantle cell lymphoma, and chronic lymphocytic leukemia/small lymphocytic lymphoma. Whereas previously published studies have generally analyzed the gene expression profiles of one type of SBCL, work presented in this paper was intended to identify genes that are differentially expressed between three SBCL subtypes. This analysis was performed using mRNA pooled from multiple specimens representing each tissue type. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was used to validate the differential expression of 23 of these genes. Among the 23 validated genes were cyclin D1 (CCND1) and B-cell CLL/lymphoma 2, which have well-known roles in lymphoma pathogenesis. The remaining 21 genes have no currently established role in lymphoma development. Using qRT-PCR, the expression of CCND1 and seven additional genes was further studied in a panel of individual specimens. Genes identified in this study are of biological interest and represent candidate diagnostic markers.

An improved method for detecting red cells with hemoglobin H inclusions that does not require glass capillary tubes.

alpha-Thalassemia trait is the most common inherited abnormality worldwide. Diagnosis of alpha-thalassemia trait can be difficult as there are no abnormalities detectable by hemoglobin electrophoresis or high-performance liquid chromatography. Detection of individuals with alpha-thalassemia trait, particularly the type present in many Asian populations, is important for genetic counseling purposes, because these individuals are at risk for having offspring with hemoglobin Bart's hydrops fetalis, a fatal condition. The best routine diagnostic method to detect individuals with alpha-thalassemia trait is staining reticulocyte-enriched red cell preparations with brilliant cresyl blue to detect hemoglobin H inclusions. Current methods use centrifugation of microhematocrit tubes to enrich for reticulocytes, which presents a laboratory safety hazard. In this report, we describe an alternative technique to enrich for reticulocytes that does not require glass capillary tubes, but is as effective as the capillary tube method for reticulocyte enrichment and detection of cells containing hemoglobin H inclusions.

Alterations in T cell phenotype and human immunodeficiency virus type 1-specific cytotoxicity after potent antiretroviral therapy.

Cytotoxic T lymphocytes (CTLs) are an important defense against human immunodeficiency virus (HIV) type 1 but ultimately fail to control infection. To determine whether more efficient sustained immunity is induced by suppressing replication, the evolution of T cell phenotypes and HIV-specific CD8+ lymphocytes was prospectively investigated in 41 patients initiating combination therapy. Suppression of viremia to <200 copies/mL was associated with increases in naive cells (CD45RA+62L+) and declines in activated T cells (CD95+ cell counts and CD38+ HLA-DR+). HIV-specific tetramer-staining CD8+ T cells were detected in 6 of 10 HLA-A*0201-positive persons, which declined in 5 with treatment. CTL precursor frequencies were markedly consistent before and after treatment. Eight (72%) of 11 recognized > or =1 immunodominant epitope, representing either a new or an increased CTL response after treatment. Thus, activated CD8+ T cells, including those recognizing immunodominant epitopes, decline with combination therapy. However, the overall level of antigen-specific cells that are capable of differentiating into effectors remains stable, and the recognition of new epitopes may occur.

T-cell clonality determination using polymerase chain reaction (PCR) amplification of the T-cell receptor gamma-chain gene and capillary electrophoresis of fluorescently labeled PCR products.

We compared the effectiveness of polymerase chain reaction (PCR) and DNA blot analysis (DBA) for detecting clonal T-cell populations and investigated whether a nonradioactive PCR method could be used in routine clinical diagnosis. We analyzed DNA from 117 cases for T-cell clonality by PCR amplification. DBA was performed on 77 of these cases. Denaturing polyacrylamide gel electrophoresis (PCR-PAGE) of radiolabeled PCR products and capillary electrophoresis (PCR-CE) of fluorescently labeled PCR products were used for PCR product separation and quantitation. Complete agreement was obtained between PCR-PAGE and DBA in 67 of 77 cases. One case was positive by DBA and negative by PCR-PAGE, and 3 cases were positive by PAGE and negative by DBA. Five cases indeterminate by DBA were positive by PCR-PAGE, and 1 indeterminate case was negative by PCR-PAGE. In the comparison of PCR-PAGE and PCR-CE, of 63 cases with height ratios less than 2.0, all were negative by PCR-PAGE. Of 52 cases with height ratios of 2.0 or more, 50 were positive by PCR-PAGE. We conclude that PCR-CE is analytically equivalent to DBA and PCR-PAGE for detecting clonal T-cell populations. The PCR-CE method is semiquantitative and, therefore, may be more objective than gel-based methods.

Multisite comparison of CD4 and CD8 T-lymphocyte counting by single- versus multiple-platform methodologies: evaluation of Beckman Coulter flow-count fluorospheres and the tetraONE system. The NIAID DAIDS New Technologies Evaluation Group.

New analytic methods that permit absolute CD4 and CD8 T-cell determinations to be performed entirely on the flow cytometer have the potential for improving assay precision and accuracy. In a multisite trial, we compared two different single-platform assay methods with a predicate two-color assay in which the absolute lymphocyte count was derived by conventional hematology. A two-color method employing lymphocyte light scatter gating and Beckman Coulter Flow-Count fluorospheres for absolute counting produced within-laboratory precision equivalent to that of the two-color predicate method, as measured by coefficient of variation of replicate measurements. The fully automated Beckman Coulter tetraONE System four-color assay employing CD45 lymphocyte gating, automated analysis, and absolute counting by fluorospheres resulted in a small but significant improvement in the within-laboratory precision of CD4 and CD8 cell counts and percentages suggesting that the CD45 lymphocyte gating and automated analysis might have contributed to the improved performance. Both the two-color method employing Flow-Count fluorospheres and the four-color tetraONE System provided significant and substantial improvements in between-laboratory precision of absolute counts. In some laboratories, absolute counts obtained by the single-platform methods showed small but consistent differences relative to the predicate method. Comparison of each laboratory's absolute counts with the five-laboratory median value suggested that these differences resulted from a bias in the absolute lymphocyte count obtained from the hematology instrument in some laboratories. These results demonstrate the potential for single-platform assay methods to improve within-laboratory and between-laboratory precision of CD4 and CD8 T-cell determinations compared with conventional assay methods.

Use of green fluorescent protein/Flp recombinase fusion protein and flow cytometric sorting to enrich for cells undergoing Flp-mediated recombination.

Flp recombinase has been used extensively for in vivo manipulation of eukaryotic DNA at specific sequences designated as FRT sites. We developed a method to use Flp-mediated recombination without the need for drug resistance or metabolic selection of cells in which recombination has occurred. We generated expression plasmids directing expression of fusion proteins consisting of Flp recombinase and green fluorescent protein (GFP) coding sequences. When the plasmids were introduced into K562 cells containing Flp recombinase substrates and transfected cells were selected for by flow cytometric sorting, GFP-positive cells were enriched 5- to 30-fold for Flp-mediated recombination events compared with unsorted cells. These studies demonstrate the usefulness of GFP/Flp recombinase fusion proteins to manipulate chromosomal DNA in vivo without requiring drug resistance or metabolic marker genes.

Tyrosine 462 of the membrane-proximal F'-G' loop of murine Mpl is not essential for high-affinity binding of thrombopoietin.

The ligand binding site of Mpl, the thrombopoietin (Tpo) receptor, has not been determined. Tyr(462)of murine Mpl corresponds to Tyr(421)of the common beta chain of the human IL-3, IL-5 and GM-CSF receptors. Tyr(421)has been identified as essential for high-affinity ligand binding. To determine whether Tyr(462)is similarly required for Tpo binding, wild-type murine Mpl (Mpl-WT) or mutant receptors containing an alanine (Y462A) or lysine (Y462K) in place of Tyr(462)were expressed in BaF3 cells. In proliferation studies, the Y462A mutation had no effect on Tpo-induced growth. In contrast, the Y462K mutation led to an attenuated proliferative response to Tpo. In single-point binding studies, both Mpl-WT and Y462A cells were able to bind [(125)I]Tpo in a specific manner. In contrast, there was a marked reduction in binding of [(125)I]Tpo by Y462K cells. Mpl-WT cells bound Tpo with a K(d)of approximately 330 pM, while Y462A cells bound Tpo with a K(d)of approximately 268 pM. The binding affinity of Y462K cells was below that quantifiable by Scatchard analysis. This study suggests that unlike the corresponding Tyr(421)of the common human beta chain, Tyr(462)of murine Mpl is not required for high-affinity ligand binding, although it may be located in proximity to the ligand binding site.

V(D)J rearrangement in Nijmegen breakage syndrome.

Repair of DNA double-strand breaks is essential for maintenance of genomic stability, and is specifically required for rearrangement of immunoglobulin (Ig) and T cell receptor (TCR) loci during development of the immune system. Abnormalities in these repair processes also contribute to oncogenic chromosomal rearrangements that underlie many lymphoid malignancies. Nijmegen breakage syndrome (NBS) is a rare autosomal recessive condition characterized by immunodeficiency, radiation sensitivity, and increased predisposition to lymphoid cancers bearing oncogenic Ig and TCR locus translocations. NBS patients fail to produce nibrin, a protein required for the nuclear localization and function of a DNA repair complex that includes Mre11 and Rad50. Mre11 has biochemical properties that suggest a potential role in V(D)J recombination. We studied V(D)J recombination in NBS cells in vitro and in vivo, using cell lines and peripheral blood leukocyte DNA from NBS patients. We found that NBS cells were competent to rejoin signal substrates with normal efficiency and high fidelity. Coding substrates were similarly rejoined efficiently, and coding end structures appeared normal. In B cells from NBS patients, the spectrums of IgH CDR3 regions were diverse and normally distributed. Moreover, the lengths and composition of Igkappa VJ joins and IgH VDJ joins derived from NBS and normal subjects were indistinguishable. Our data indicate that nibrin plays no essential role in V(D)J recombination and is not required for the generation of an apparently diverse B cell repertoire.

Refrigerated storage improves the stability of the complete blood cell count and automated differential.

A CBC count was performed on 113 random patient and 21 control specimens before and after 24-hour room temperature (RT) storage; 98 random patient and 20 control specimens also were analyzed before and after 24 hour 4 degrees C storage. The Cell-Dyn 3500 (Abbott Laboratories, Abbott Park, IL) was used for analysis. RT storage showed a decline in WBC count using the optical but not the impedance method, resulting in a large number of WBC flags. An increase in mean corpuscular volume also was seen for patient specimens. The automated WBC differential showed a decrease in the percentage of neutrophils and an increase in the percentage of lymphocytes, owing primarily to neutrophil degeneration. These changes also were seen in the manual differential to a similar degree. Storage of specimens at 4 degrees C largely prevented all of these changes. The implementation of refrigerated specimen storage is a simple, inexpensive method to improve the accuracy of CBC results for aged specimens on automated hematology analyzers.

DNA-protein interactions in the proximal zeta-globin promoter: identification of novel CCACCC- and CCAAT-binding proteins.

The human zeta-globin gene is expressed in a tissue- and developmental-specific pattern, with expression confined to primitive erythroid cells of the embryonic yolk sac blood islands. Transgenic mouse studies have shown that the proximal zeta-globin promoter contains sequences that contribute to the stage-specificity of expression, but no systematic functional studies of the cis elements in the proximal zeta-globin promoter have been reported. In this paper, we show that a number of conserved sequence elements in the zeta-globin promoter are important for promoter activity in transiently transfected K562 erythroleukemia cells, which constitutively express zeta-globin. These include a GATA site at -105, a CCACC site at -93, a CCAAT box at -65, and a TATA box at -29. A highly conserved CCTCC sequence at -78 is not important for zeta-globin promoter activity in this system. Mutations at these sites do not result in increased promoter activity in OCIM1 cells, an erythroid line that does not express zeta-globin, suggesting none of these sites is a developmental silencer. Electrophoretic mobility shift assays show that K562 and OCIM1 nuclear extracts contain DNA-binding activities that interact with the -105 GATA, -65 CCAAT, and -29 TATA sites. In addition K562 cells, but not OCIM1 cells, have an activity that binds the -93 CCACC site. GATA-1 interacts with the GATA site. The K562 CCACC-binding protein is distinct from Sp1, Sp2, Sp3, Sp4, EKLF, and BKLF. A specific -65 CCAAT-binding activity is present in K562 and OCIM1 nuclear extracts that is distinct from other CCAAT-binding proteins including CBF/NF-Y, C/EBP, NF-1, and CP2. Thus, we have identified two novel factors that may contribute to the tissue or developmental stage-specific expression of zeta-globin.

Interferon-alpha treatment of posttransplant lymphoproliferative disorder in recipients of solid organ transplants.

Posttransplant lymphoproliferative disorder (PTLD) has been treated with decreased immunosuppression, antiviral medications, anti-B lymphocyte agents, radiation therapy, and/or chemotherapy. However, a standardized stepwise approach to treatment has not been previously evaluated. In the present study, 19 consecutive patients presenting to a single institution with newly diagnosed PTLD were treated according to a sequential protocol that consisted of (1) a reduction in immunosuppressive medications plus, if feasible, resection or definitive radiation therapy of localized disease, (2) interferon-alpha, and (3) systemic chemotherapy. Of the 3 patients presenting exclusively with localized disease, two were treated with resection of pulmonary parenchymal nodules and one was treated with radiation therapy to a paraspinous mass, without evidence of recurrence at a mean follow-up of 31 months (range, 8 to 46 months). Sixteen patients presented with PTLD not amenable to local therapy, and they were treated daily with 3x10(6) units/m2 subcutaneous interferon-alpha. Total regression of PTLD (defined as disappearance of the tumor mass by physical examination or computed tomography scanning) was found in 8 of 14 patients who received at least 3 weeks of interferon therapy. Interferon-alpha therapy was continued for 6 to 9 months in the eight patients judged to be responders. None of these patients have relapsed to date with the same neoplastic clone. Two patients, however, developed new neoplastic clones. Seven patients received systemic chemotherapy with CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone) (n=1), EPOCH (etoposide, vincristine, and doxorubicin administered as a continuous infusion, with an intravenous bolus of cyclophosphamide and oral prednisone) (n=4), or EPOCH followed by DHAP (dexamethasone, cytarabine, and cisplatin) (n=2) after failure of interferon-alpha; five patients had a complete response. Only 1 of the 19 patients died of uncontrolled PTLD. These results suggest that the majority of solid organ transplant recipients who develop PTLD can be safely and successfully treated using a sequential approach to therapy.

Structure and function of the zeta-globin upstream regulatory element.

The human zeta-globin promoter contains a strong positive regulatory element in the 5' flanking region, designated the zeta-globin upstream regulatory element (URE). In this study, we define the minimal sequences required for URE function and characterize the associated protein-DNA interactions. Deletion experiments show that the URE spans a 60 bp region located between 220 and 279 bp 5' to the transcription start site. Further subdivision of this region shows that multiple cis acting sequences are present. Electrophoretic mobility shift assays demonstrate that the erythroid transcription factor GATA-1 binds a site at -230, and Sp1 and an unidentified factor bind a CCACC site at -240. The unidentified CCACC factor is distinct from two other CCACC factors, EKLF and BKLF/TEF-2. A third complex contains a novel DNA-binding activity that interacts with a site in the -269 to -255 region, designated URE binding factor (URE-BF). This factor is present in K562 cells that express zeta-globin, but is absent in the OCIM1 cell line, a human erythroid cell line that does not express zeta-globin. URE-BF appears to interact with a GATA factor, since formation of the URE-BF complex can be prevented by the presence of unlabeled oligonucleotides containing GATA sites. Finally, increasing the distance from the -230 GATA site to the two upstream sites causes a progressive decrease in zeta-globin promoter activity. There is no indication of a requirement for GATA-1 to be on the same side of the DNA helix as the other upstream factors. These results show that zeta-globin promoter function is highly dependent on a 60 bp region to which at least three different factors bind. Two of these factors may represent DNA-binding proteins not previously identified as important for regulation of globin gene expression. It is likely that these factors interact physically to create a functional regulatory unit.

A family inheriting different subtypes of acute myelogenous leukemia.

Rare inherited cancer syndromes have proven invaluable for the identification of genes involved in the more frequent corresponding noninherited cases. We report on a family with an adult onset, incompletely penetrant, autosomal dominant syndrome of myelodysplasia and acute myelogenous leukemia, affecting at least eight, and probably ten, individuals from three generations. The patients have developed leukemias differing in morphologic subtype, tumor cytogenetics, and abruptness of presentation. Some have presented with acute onset and others with protracted myelodysplasia. This family does not have an unusual incidence of other malignancies; however, one person at 50% risk of inheriting this gene developed atypical mycobacterium infection in the absence of leukemia, but also without appreciable risk factors for acquired deficiencies in cellular immunity. Features common to affected family members, including the individual with mycobacterium infection, are the early presence in the bone marrow of red cell and platelet maturation defects. A search for mutations in diseased marrows fails to detect abnormalities of p53 or N-ras. Two of the affected family members, third degree relatives, have co-inherited a constitutional chromosomal banding variation of 9p21-22, potentially suggesting linkage to this locus. The variable penetrance and expressivity of this syndrome support a multistep model of leukemia evolution, in which the gene defined by this family's syndrome is the signal step.

Oral presentation of posttransplantation lymphoproliferative disorders. An unusual manifestation.

Cyclosporine, an immunosuppressive agent widely used in organ transplantation, has several undesirable side effects, including gingival hyperplasia, which occurs in up to 70% of patients. Another complication associated with use of cyclosporine and other immunosuppressants is an increased incidence of malignancies. Long-term use of cyclosporine also is associated with a spectrum of hyperproliferative disorders ranging from reactive lymphoid hyperplasia to aggressive malignant lymphomas. While cyclosporine-related lymphoproliferative disorders have been widely reported, they have not been described in the oral cavity as the first manifestation of this disease. We report on two cardiac transplantation patients with a history of cyclosporine use who presented initially with oral symptoms of lymphoproliferative disorder. Both had erythematous to cyanotic and hyperplastic gingiva. On gingivectomy, the fixed tissue was soft, glistening, and tan colored, in contrast to the usual firm, white, cyclosporine-associated, benign gingival fibrous hyperplasia. Histologically, a dense, diffuse infiltrate of lymphoplasmacytoid cells with vesicular nuclei, prominent nucleoli, a moderate amount of cytoplasm, and high mitotic activity was observed. Immunocytochemical studies confirmed that the cells were monoclonal for lambda light chains in one patient and kappa light chains in the other. The cells from one patient were positive for CD45, while both patients were negative for CD20 and all nonhematopoietic antigens tested. Both tissues were strongly positive for Epstein-Barr virus. Morphology and immunocytochemistry findings are consistent with a posttransplant lymphoproliferative disorder. These are the first two reported cases of cyclosporine-associated posttransplant lymphoproliferative disorders presenting as gingival hyperplasia.

Murine thrombopoietin mRNA levels are modulated by platelet count.

The activity of the c-Mpl ligand hematopoietic progenitors meets criteria expected for thrombopoietin (TPO). Bio-assays have shown that blood TPO levels are inversely related to platelet mass. We sought to identify the molecular basis for this regulation. To determine if TPO mRNA levels respond to platelet demand, RNA from selected organs of mice with high, normal or low platelet counts was subjected to semiquantitative reverse transcriptase-polymerase chain reaction. Although no differences in TPO mRNA levels between control and treated mice could be detected in liver or kidney, TPO-specific bands were more intense after 25 to 30 polymerase chain reaction cycles in marrow-derived mRNA from thrombocytopenic mice. The TPO-specific bands were less intense in thrombocytotic mouse marrow and spleen than control mouse marrow and spleen after 30 cycles. These data support the hypothesis that TPO levels are regulated, at least in part, by modulating mRNA levels in response to platelet demand.